Yes, merits are for new characters to be able to skip up difficulties - either up to Elite from Normal or up to Ultimate from Normal/Elite. Characters that have already reached a higher difficulty can’t use a merit token for that difficulty.
Far as I can recall this is right - 2 to 50 was 3 skill points and then from 51 to 85 (base game max level) you got 2. With the Ashes expansion increasing the max level to 100 this was changed to 3 up to 50, 2 up to 90 and then just 1 point from 91 to 100. Then there are the extra points you can get from doing some quests in the game. Have you actually done the expansions through Normal, Elite and Ultimate to try and get those extra points?
Whether that all adds up to your missing points though …
Could just be that the character is so old it’s not working properly.